It depends on how you like to get stuff into EagleFiler. Personally, I usually import via the Capture with options key, so it’s easy to add tags at that time. Likewise if you create the documents from within EagleFiler. If you tend to import by saving files into the “To Import” folder, you could use Default Folder to add the tags right from the Save dialog. Tags might be useful if you do significant work with the files in the Finder before putting them into EagleFiler. If you’re the type of person who wants to just dump everything into the library and tag/organize it later, then you would just do the tagging in EagleFiler. So I think it’s simplest to do everything in one application, but depending on your workflow you may find additional software helpful.
From a user perspective, it’s an implementation detail that makes little difference. OpenMeta stores tags in the extended attributes, which is faster and more reliable than the Spotlight comments. (For the EagleFiler user, this makes little difference because its database is even faster and more reliable.) Secondly, the extended attributes are a much nicer system for developers, and so hopefully it will increase the amount of software that can interoperate.